Current questions and answers regarding the map editor.

Hmm... I recently edited textures in Paint.NET, and everything changed perfectly (became transparent). I don't think Photoshop is worse than Paint.NET.

Photoshop is better, but Paint.NET isn't cluttered with all sorts of unnecessary features that not everyone needs. Because it's "lightweight" and free, it's a good choice if you're not interested in photo editing. ;)
In Photoshop, you also need to install an additional plugin for DDS, which isn't convenient for everyone.

I'm 99% sure that you can make things transparent in Photoshop.

And I'm 100% sure :D